STEP 1

In order to find start/end positions of aligned sequences, 1.find_position_bam.cpp needs to be compiled into binary. By running build_find_position_bam.sh , it will firstly automatically download and compile bamtools library (https://github.com/pezmaster31/bamtools) and secondly compile 1.find_position_bam.cpp into binary.
To build bamtools library properly, cmake, g++, and git should be pre-installed.

STEP 2

Set an environment variable 'DIGENOME_HOME', to the directory which contains python files and executables.

STEP 3

Copy digenome-run script to bin directory (i.e. ~/bin), and run the script to analyze BAM file, as below:

STEP 4 - Usage

Before running digenome-seq, please type digenome-run -h or --help for help message.